Where does mediator bind in vivo?
Where does mediator bind in vivo?
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DOI：
10.1371/journal.pone.0005029
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Struhl K
中科院分区：
文献类型：
--
作者：
Fan X;Struhl K
介体复合物与 RNA 聚合酶 (Pol) II 结合，并在适当的环境条件下被激活蛋白招募到增强子区域。然而，酵母细胞中介体关联的问题存在争议。在最佳生长条件（YPD 培养基）下，我们基本上无法在任何酿酒酵母启动子区域检测到介体，包括那些支持非常高水平转录的启动子区域。相比之下，在合成完整（SC）培养基中进行的全基因组微阵列实验表明，Mediator 与启动子和编码区的许多基因相关。通过染色质免疫沉淀分析，我们发现 SC 培养基中存在少量在 YPD 培养基中未观察到的介体靶标。然而，在全基因组分析中发现的大多数介导目标都是误报，这是由于几个相互关联的原因引起的：使用过于宽松的截止值；未标记菌株中不同基因组区域之间表观 IP 效率的人为差异；低倍数富集使得很难区分真正的介体靶标和在没有标记的介体蛋白的情况下发生的假阳性。最后，高活性编码区中明显的介体关联是由于缺乏核小体而对可及性产生非特异性影响，而不是介体的特定关联。这些结果表明，Mediator 并不与酵母基因组中的许多位点结合，而是以激活子和应激特异性的方式选择性地与有限数量的上游启动子区域结合。
The Mediator complex associates with RNA polymerase (Pol) II, and it is recruited to enhancer regions by activator proteins under appropriate environmental conditions. However, the issue of Mediator association in yeast cells is controversial. Under optimal growth conditions (YPD medium), we were unable to detect Mediator at essentially any S. cerevisiae promoter region, including those supporting very high levels of transcription. In contrast, whole genome microarray experiments in synthetic complete (SC) medium reported that Mediator associates with many genes at both promoter and coding regions. As assayed by chromatin immunoprecipitation, we show that there are a small number of Mediator targets in SC medium that are not observed in YPD medium. However, most Mediator targets identified in the genome-wide analysis are false positives that arose for several interrelated reasons: the use of overly lenient cut-offs; artifactual differences in apparent IP efficiencies among different genomic regions in the untagged strain; low fold-enrichments making it difficult to distinguish true Mediator targets from false positives that occur in the absence of the tagged Mediator protein. Lastly, apparent Mediator association in highly active coding regions is due to a non-specific effect on accessibility due to the lack of nucleosomes, not to a specific association of Mediator. These results indicate that Mediator does not bind to numerous sites in the yeast genome, but rather selectively associates with a limited number of upstream promoter regions in an activator- and stress-specific manner.
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影响因子：
9.8
作者：
Li XY;MacArthur S;Bourgon R;Nix D;Pollard DA;Iyer VN;Hechmer A;Simirenko L;Stapleton M;Luengo Hendriks CL;Chu HC;Ogawa N;Inwood W;Sementchenko V;Beaton A;Weiszmann R;Celniker SE;Knowles DW;Gingeras T;Speed TP;Eisen MB;Biggin MD
通讯作者：
Biggin MD
DOI：
10.1073/pnas.92.10.4587
发表时间：
1995-05-09
影响因子：
11.1
作者：
THOMPSON, CM;YOUNG, RA
通讯作者：
YOUNG, RA
影响因子：
16
作者：
Pokholok, DK;Hannett, NM;Young, RA
通讯作者：
Young, RA
影响因子：
7
作者：
Tanay, Amos
通讯作者：
Tanay, Amos
影响因子：
2.6
作者：
SCHNEIDER, BL;SEUFERT, W;FUTCHER, AB
通讯作者：
FUTCHER, AB